# About me .pull-left[ <img src="data:image/png;base64,#images/hello.jpg" width="400px" style="display: block; margin: auto;" /> .center[ my name is .large[Shaun Nielsen] ] * [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M352 256c0 22.2-1.2 43.6-3.3 64H163.3c-2.2-20.4-3.3-41.8-3.3-64s1.2-43.6 3.3-64H348.7c2.2 20.4 3.3 41.8 3.3 64zm28.8-64H503.9c5.3 20.5 8.1 41.9 8.1 64s-2.8 43.5-8.1 64H380.8c2.1-20.6 3.2-42 3.2-64s-1.1-43.4-3.2-64zm112.6-32H376.7c-10-63.9-29.8-117.4-55.3-151.6c78.3 20.7 142 77.5 171.9 151.6zm-149.1 0H167.7c6.1-36.4 15.5-68.6 27-94.7c10.5-23.6 22.2-40.7 33.5-51.5C239.4 3.2 248.7 0 256 0s16.6 3.2 27.8 13.8c11.3 10.8 23 27.9 33.5 51.5c11.6 26 20.9 58.2 27 94.7zm-209 0H18.6C48.6 85.9 112.2 29.1 190.6 8.4C165.1 42.6 145.3 96.1 135.3 160zM8.1 192H131.2c-2.1 20.6-3.2 42-3.2 64s1.1 43.4 3.2 64H8.1C2.8 299.5 0 278.1 0 256s2.8-43.5 8.1-64zM194.7 446.6c-11.6-26-20.9-58.2-27-94.6H344.3c-6.1 36.4-15.5 68.6-27 94.6c-10.5 23.6-22.2 40.7-33.5 51.5C272.6 508.8 263.3 512 256 512s-16.6-3.2-27.8-13.8c-11.3-10.8-23-27.9-33.5-51.5zM135.3 352c10 63.9 29.8 117.4 55.3 151.6C112.2 482.9 48.6 426.1 18.6 352H135.3zm358.1 0c-30 74.1-93.6 130.9-171.9 151.6c25.5-34.2 45.2-87.7 55.3-151.6H493.4z"/></svg> shaunnielsen.com.au](https://shaunnielsen.com.au) * [<svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg> @Shaunson26](https://github.com/Shaunson26) * [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg> shaunson26@gmail.com](mailto:shaunson26@gmail.com) ] .pull-right[ ### Experience **Data Science and Engineering Consultant** **R tutor** Applied Epi **Senior Data Analyst** - Government public health **Biostatistican** - Government public health **Postdoctural researcher** - Microbial ecology </br> </br> <div style="display: flex;align-items: center;justify-content: space-between"> <img src="data:image/png;base64,#images/NSW-logo-and-health-descriptor-large.png" width="100px" /> <img src="data:image/png;base64,#images/unsw.png" width="100px" /> <img src="data:image/png;base64,#images/applied-epi.png" width="100px" /> <img src="data:image/png;base64,#images/cnb-logo.png" width="100px" /> </div> ] --- # Course objective .center[.large[ Give you experience across the scientific data analysis pipeline using R and RStudio ]] <div class="figure" style="text-align: center"> <img src="data:image/png;base64,#images/course-data-science-process.png" alt="Image adapted from R for Data Science" width="70%" /> <p class="caption">Image adapted from R for Data Science</p> </div> -- .center[.large[ so you can continue to build a foundation and work independently (and collaboratively) ]] -- - Make using R less daunting - Ability to apply tasks from others resources (books, tutorials, etc) - Build a foundation for more complex applications - Troubleshoot common R and analysis problems --- # Learning - R is a skill <style type="text/css"> .practice-practice { position: absolute; bottom: 5%; right: 2%; width: 300px; } </style> .. like learning a new language or musical instrument - **Practice regularly** .. the more you do, the more you learn - **Repetition is key** .. repeatedly using commands and techniques solidifies understanding and improves retention - **Experiment and explore** .. try modifying code examples and exploring different functions. See what happens! - **Do not be afraid of making mistakes** .. helps you understand how R works. Do not get discouraged by errors. Search for solutions and learn from them </br> </br> -- This is a relatively **short course** - There is lots of information to cover - Goal is to **expose you broadly to topics** .. you **must** practice and repeat! - The timing between sessions (2 days / week for 2 weeks) give you time! .practice-practice[ <!-- --> ] --- # Course outline .pull-left[ ## Module 1 - first steps - Using R and RStudio - Coding basics - Data types and structures - R packages - Importing data ] -- .pull-right[ ## Module 2 - data manipulation - Manipulating and transforming data - Joining data - Reshaping data ] -- .pull-left[ ## Module 3 - data visualisation - Visualising data - Creating different plot types - Exporting plots ] -- .pull-right[ ## Module 4 -basic statistics - t-tests - ANOVA - Linear models ] --- # Course structure **Short lectures**: 5 - 20 min -- **Exercises**: 20 - 30 min -- - Simple responses .pull-left[ ``` r # Calculate the log of 4.5 _ ``` ] -- .pull-right[ ``` r # Calculate the log of 4.5 log(4.5) ``` ] -- - To more complex code .pull-left[ ``` r # Obtain the total cases and deaths by country # and year. There should not be any NA values covid %>% _ ``` ] -- .pull-right[ ``` r # Obtain the total cases and deaths by country # and year. There should not be any NA values covid %>% group_by(country) %>% summarise(total_cases = sum(cases), ...) ``` ] -- **Discussion of exercises**: 5 - 10 min -- **Small project**: Provided at the start of course and submitted within 1 week after the course. --- # Course dates and times We have **4 days** - 19, 21, 27 ad 29 May - 2 days / week over 2 weeks - Gives time for you to revise content and ask questions <br> A total of **13 hours** (14 including breaks) - 3.5 hours per day (3.25 hours + 15 min break time) - 9:30 a 13.00 <br> We will work through parts of modules and stop when necessary - 10 - 30 min per module sub-section --- # Course references - R for Data Science (book/online) - https://r4ds.hadley.nz/ - Introductory Statistics with R (book) - [link to pdf](https://www.academia.dk/BiologiskAntropologi/Epidemiologi/PDF/Introductory_Statistics_with_R__2nd_ed.pdf) - Environmental computing (online) - https://environmentalcomputing.net/ - The Edpidemiologist R hanbook (online) - [English](https://epirhandbook.com/en) / [Spanish](https://epirhandbook.com/es) <br> <br> .pull-left[ .pull-left[ <img src="data:image/png;base64,#images/rd4s.jpg" height="200px" style="display: block; margin: auto;" /> ] .pull-right[ <img src="data:image/png;base64,#images/intro-stats.png" height="200px" style="display: block; margin: auto;" /> ] ] .pull-right[ .pull-left[ <img src="data:image/png;base64,#images/epi-handbook.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ <img src="data:image/png;base64,#images/env-comp.png" height="200px" style="display: block; margin: auto;" /> ] ] --- # Have you setup your computer? Open RStudio now ... - Installed **R**, **RStudio** and **git** - Started an RStudio project with the link - https://github.com/Shaunson26/r-for-scientific-research - **Open RStudio** using the `r-for-scientific-research.Rproj`. - You should be working within the course project throughout the course. <img src="data:image/png;base64,#images/rproject-started.png" width="100%" style="display: block; margin: auto;" /> --- # Downloading course content I will release module content sequentially. It can be download using the **git** panel and **pull** <img src="data:image/png;base64,#images/git-pull.png" style="display: block; margin: auto;" /> --- # Research field and R use survey I created a survey to capture information about your research field, data use and experience with R - https://forms.gle/VUGScKHPSLaKn28p8 - I will create a simple analysis with this data and share it with you during the course <img src="data:image/png;base64,#images/google-form.png" width="500px" style="display: block; margin: auto;" /> --- class: middle # Let's begin!